I don't think he even knows Eleanor. Even when he lied, he only claimed to have recognized Henry, accompanied by a young woman he assumed to be his sister. Thorpe saw Catherine dancing with Henry, but probably can't claim to know Miss Tilney (he would probably lie about it if he could, right?).

So when he sees a girl looking at Catherine, he makes a casual remark. He probably only had a glance of Miss Tilney while the gig was going by and didn't notice Mr Tilney with her.